Ecosyste.ms: Papers

10.1016/j.dib.2016.01.016

Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor
Cited by: 5
Author(s): Nitin Chitranshi, Vivek Kumar Gupta, Yogita Dheer, Veer Bala Gupta, Roshana Vander Wall, Stuart L. Graham
Software Mentions: 3
Published: over 8 years ago

10.1107/S1744309113012931

Structure of PatF from<i>Prochloron didemni</i>
Cited by: 26
Author(s): Andrew F. Bent, Jesko Koehnke, Wael E. Houssen, Margaret Caroline MacHin Smith, Marcel Jaspars, James H. Naismith
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: almost 8 years ago

10.1093/database/bau102

PolyprOnline: polyproline helix II and secondary structure assignment database
Cited by: 35
Author(s): Romain Chebrek, Sylvain Léonard, Alexandre G. de Brevern, Jean‐Christophe Gelly
Software Mentions: 3
Published: about 10 years ago

10.3390/md16100386

Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer’s Disease: A Computational Study
Cited by: 25
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Conxita Àvila, Melchor Sánchez-Martínez
Software Mentions: 3
Published: about 6 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: over 5 years ago

10.1111/febs.15514

Structure‐based design of peptides that trigger <i>Streptococcus pneumoniae</i> cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1002085

The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment
Cited by: 34
Author(s): Stephen C. Graham, L. Peter Sarin, Mohammad W. Bahar, Robert A. Myers, David I. Stuart, Dennis H. Bamford, Jonathan M. Grimes
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0243429

A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations
Cited by: 2
Author(s): Dimitrios A. Mitsikas, Nicholas M. Glykos
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-020-01531-x

Structural insights into photoactivation of plant Cryptochrome-2
Cited by: 27
Author(s): Malathy Palayam, Jagadeesan Ganapathy, Angelica M. Guercio, Lior Tal, Samuel L. Deck, Nitzan Shabek
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-019-0427-1

Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis
Cited by: 20
Author(s): K. Grave, M.D. Bennett, Martin Högbom
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-01283-8

Structural role of essential light chains in the apicomplexan glideosome
Cited by: 8
Author(s): Samuel Pažický, Karthikeyan Dhamotharan, Karol Kaszuba, Haydyn D. T. Mertens, Tim‐Wolf Gilberger, Dmitri I. Svergun, Jan Kosiński, Ulrich Weininger, Christian Löw
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-020-01640-7

Molecular basis of IRGB10 oligomerization and membrane association for pathogen membrane disruption
Cited by: 8
Author(s): Hyekyung Ha, Hye Lin Chun, So Yeon Lee, Jin Ho Jeong, Yeon-Gil Kim, Hyun Ho Park
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-12-207

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
Cited by: 39
Author(s): Rong Liu, Jianjun Hu
Software Mentions: 2
Published: over 13 years ago

10.1107/S2053230X14003355

A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
Cited by: 13
Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: almost 11 years ago

10.1038/s42003-019-0675-0

Structural analysis identifies an escape route from the adverse lipogenic effects of liver X receptor ligands
Cited by: 14
Author(s): Anna Y. Belorusova, Emma Evertsson, Daniel Hovdal, Jenny Sandmark, Emma Bratt, Ingela Maxvall, Ira G. Schulman, Peter Åkerblad, Eva-Lotte Lindstedt
Software Mentions: 2
Published: almost 5 years ago

10.1038/s42003-021-02326-4

Structure-based insights into evolution of rhodopsins
Cited by: 13
Author(s): Dmitrii Zabelskii, Natalia I. Dmitrieva, Oleksandr Volkov, Vitaly Shevchenko, Kirill Kovalev, Taras Balandin, Dmytro Soloviov, Roman Astashkin, Egor V. Zinovev, Alexey Alekseev, Ekaterina Round, Vitaly Polovinkin, Igor Chizhov, Andrey Rogachev, Ivan Okhrimenko, Valentin Borshchevskiy, Vladimir Chupin, Georg Büldt, Natalia Yutin, Ernst Bamberg, Eugene V. Koonin, Valentin Gordeliy
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-020-0882-8

Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses
Cited by: 33
Author(s): Daisuke Oikawa, Yusuke Sato, Fumiaki Ohtake, Keidai Komakura, Kazuki Hanada, Koji Sugawara, Seigo Terawaki, Yukari Mizukami, Hoang T. Phuong, Kiyosei Iio, Shingo Obika, Masaya Fukushi, Takashi Irie, Daisuke Tsuruta, Shinobu Sakamoto, Keiji Tanaka, Yasushi Saeki, Shuya Fukai, Fuminori Tokunaga
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-018-0262-9

Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters
Cited by: 19
Author(s): Yong Wei, Zi Jian Xiong, Jun Li, Chunxia Zou, Christopher W. Cairo, John S. Klassen, Gilbert G. Privé
Software Mentions: 2
Published: almost 6 years ago

10.1107/S2053230X19012172

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
Cited by: 3
Author(s): Eric Montemayor, Johanna M Virta, Lauren D. Hagler, Steven C. Zimmerman, Samuel E. Butcher
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-02473-8

The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon
Cited by: 4
Author(s): Yuya Taguchi, Tomohiro Yamasaki, Marie Ishikawa, Yuki Kawasaki, Ryuji Yukimura, Maki Mitani, Kunio Hirata, Daisuke Kohda
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-020-01147-1

Molecular basis of the lipid-induced MucA-MucB dissociation in Pseudomonas aeruginosa
Cited by: 6
Author(s): Tao Li, Libang He, Changcheng Li, Mei Kang, Yingjie Song, Yuanfeng Zhu, Yanjiao Shen, Ninglin Zhao, Chang Zhao, Jing Yang, Qin Huang, Xingyu Mou, Aiping Tong, Jinliang Yang, Zhenling Wang, Chengjie Ji, Hong Li, Hong Tang, Rui Bao
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-020-01633-6

Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites
Cited by: 3
Author(s): Meng-Hsuan Lin, Chao-Cheng Cho, Yi‐Chih Chiu, Chia‐Yu Chien, Yiping Huang, Chi‐Fon Chang, Chun‐Hua Hsu
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-021-01739-5

Structure–function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis
Cited by: 2
Author(s): Hiroyuki Kajiura, Takumi Yoshizawa, Yuji Tokumoto, Nobuaki Suzuki, Shinya Takeno, Kanokwan Jumtee Takeno, Takuya Yamashita, Shun‐ichi Tanaka, Yoshinobu Kaneko, Kazuhito Fujiyama, Hideki Matsumura, Yasuhiro Nakazawa
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-020-01266-9

Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy
Cited by: 17
Author(s): Hyunjin Cho, Yuri Choi, Kyoung‐Wook Min, Jung Bae Son, Hyojin Park, Hyung Ho Lee, Seokhee Kim
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-018-0236-y

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release
Cited by: 19
Author(s): Heidi B. Cao, Mu Gao, Hongyi Zhou, Jeffrey Skolnick
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.clim.2015.05.020

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders
Cited by: 84
Author(s): Pauline A. van Schouwenburg, Emma E Davenport, Anne‐Kathrin Kienzler, Ishita Marwah, Benjamin Wright, Mary Lucas, Tomas Malinauskas, Hilary C. Martin, Helen Lockstone, Jean‐Baptiste Cazier, Helen Chapel, Julian C. Knight, Smita Y. Patel
Software Mentions: 2
Published: about 9 years ago

10.1038/s42003-020-01546-4

Structural basis of Naa20 activity towards a canonical NatB substrate
Cited by: 3
Author(s): Dominik Layer, Jürgen Kopp, Miriam Fontanillo, Maja Köhn, Karine Lapouge, Irmgard Sinning
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-020-01160-4

Human adiponectin receptor AdipoR1 assumes closed and open structures
Cited by: 13
Author(s): Hiroaki Tanabe, Yuki Fujii, Miki Okada-Iwabu, Masato Iwabu, Kuniyuki Kano, Hiroki Kawana, Masakatsu Hato, Yoshihiro Nakamura, Takaho Terada, Tomomi Kimura-Someya, Mikako Shirouzu, Yoshiaki Kawano, Masaki Yamamoto, Junken Aoki, Toshimasa Yamauchi, Takashi Kadowaki, Shigeyuki Yokoyama
Software Mentions: 2
Published: over 4 years ago

10.1107/S1399004715002485

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4
Cited by: 38
Author(s): Noelia Alonso-García, Inés García-Rubio, José A. Manso, Rubén M. Buey, Hector Urien, Arnoud Sonnenberg, Gunnar Jeschke, José M. de Pereda
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0052421

Head-Head Interactions of Resting Myosin Crossbridges in Intact Frog Skeletal Muscles, Revealed by Synchrotron X-Ray Fiber Diffraction
Cited by: 14
Author(s): Kazuteru Oshima, Yoshiaki Sugimoto, Thomas C. Irving, Katsuzo Wakabayashi
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0021267

Expression of Enzymatically Inactive Wasp Venom Phospholipase A1 in Pichia pastoris
Cited by: 13
Author(s): Irina Borodina, Bettina M. Jensen, Tim Wagner, Maher Abou Hachem, Ib Søndergaard, Lars K. Poulsen
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0020950

Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P8′ Residue in the Potato Inhibitor I Family
Cited by: 13
Author(s): Long Wang, Fei Zhao, Mei Li, Hongmei Zhang, Yu Gao, Peng Cao, Xiaowei Pan, Zhuanhua Wang, Wenrui Chang
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2091-12-59

Delineation of the Pasteurellaceae-specific GbpA-family of glutathione-binding proteins
Cited by: 8
Author(s): Bjorn Vergauwen, Ruben Van der Meeren, Ann Dansercoer, Savvas N. Savvides
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0043985

Stapled BH3 Peptides against MCL-1: Mechanism and Design Using Atomistic Simulations
Cited by: 37
Author(s): Thomas L. Joseph, David P. Lane, Chandra Verma
Software Mentions: 2
Published: about 12 years ago

10.1038/s42003-018-0203-7

Structural basis for activation of plasma-membrane Ca2+-ATPase by calmodulin
Cited by: 28
Author(s): Julius Nitsche, Inokentijs Josts, Johannes Heidemann, Haydyn D. T. Mertens, Selma Maric, Martine Moulin, Michael Haertlein, Sebastian Büsch, V. Trevor Forsyth, Dmitri I. Svergun, Charlotte Uetrecht, Henning Tidow
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0206143

Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7
Cited by: 7
Author(s): Masoud Lotfan, Suman Choudhary, Munna Lal Yadav, Sudarshan Kumar, Surender Singh, Shveta Bathla, Preeti Rawat, Jai K. Kaushik, Ashok Kumar Mohanty
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0081753

Heterologous Expression of Mycobacterial Esx Complexes in Escherichia coli for Structural Studies Is Facilitated by the Use of Maltose Binding Protein Fusions
Cited by: 22
Author(s): M.A. Arbing, Sammy Chan, L.R. Harris, E. Kuo, T. Zhou, Christine J. Ahn, Ludivine David NGuyen, Cyndi Qixin He, Jamie Lu, Phuong T. Menchavez, Ae Sun Shin, Thomas Holton, M.R. Sawaya, Duilio Cascio, David Eisenberg
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0067536

Towards Ligand Docking Including Explicit Interface Water Molecules
Cited by: 58
Author(s): Gordon Lemmon, Jens Meiler
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0170260

Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host
Cited by: 5
Author(s): Konstantinos Koussis, Evi Goulielmaki, Anna Chalari, Chrislaine Withers‐Martinez, Inga Sidén‐Kiamos, Kai Matuschewski, Thanasis G. Loukeris
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0231513

Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
Cited by: 8
Author(s): Keita Saito, Alexander Holm Viborg, Shiho Sakamoto, T. Arakawa, Chihaya Yamada, Kiyotaka Fujita, Shinya Fushinobu
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0062021

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding
Cited by: 20
Author(s): R. Vinaik, Guennadi Kozlov, Kalle Gehring
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0114903

An Integrative Computational Approach for Prioritization of Genomic Variants
Cited by: 7
Author(s): Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R. Paciorkowski, Ghayda Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al‐Gazali, Christopher E. Mason, M. Elizabeth Ross, Natalia Maltsev, T. Conrad Gilliam
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0251067

Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism
Cited by: 4
Author(s): Sunghoon Kwon, Hye Lin Chun, Hyekyung Ha, So Yeon Lee, Hyun Ho Park
Software Mentions: 2
Published: over 3 years ago

10.1007/s00253-021-11129-w

Assembly of a Rieske non-heme iron oxygenase multicomponent system from Phenylobacterium immobile E DSM 1986 enables pyrazon cis-dihydroxylation in E. coli
Cited by: 4
Author(s): Andreas Hunold, Wendy Escobedo‐Hinojosa, Elsa Potoudis, Daniela Resende, Theresa Farr, Per‐Olof Syrén, Bernhard Hauer
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0239702

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique
Cited by: 7
Author(s): Timothy R. Stachowski, M. Elizabeth Snell, Edward H. Snell
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0082484

Structure-Based Analysis of A19D, a Variant of Transthyretin Involved in Familial Amyloid Cardiomyopathy
Cited by: 5
Author(s): Priscila S. Ferreira, Oliveira Sant’Anna, Nathalia Varejão, Cristina Ferreira Lima, Sérgio A. P. Novis, Renata V. Barbosa, Concy M. Caldeira, Franklin David Rumjanek, Salvador Ventura, Márcia Waddington Cruz, Débora Foguel
Software Mentions: 2
Published: almost 11 years ago

10.1107/S2059798318005764

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
Cited by: 6
Author(s): Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0096809

Calponin-Like Chd64 Is Partly Disordered
Cited by: 10
Author(s): Małgorzata Kozłowska, Aneta Tarczewska, Michał Jakób, Kamil Szpotkowski, Magdalena Wojtas, Grzegorz Rymarczyk, Andrzej Ożyhar
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0029406

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
Cited by: 21
Author(s): Melanie I. Stefan, David P. Marshall, Nicolas Le Novère
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0154046

Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics
Cited by: 2
Author(s): Gloria Ruiz-Gómez, John C. Hawkins, Patrick Jenny, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, M. Teresa Pisabarro
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0123195

An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2) Selective Agonist
Cited by: 12
Author(s): Nadendla EswarKumar, Catherine Teyssier, V. Delfosse, Valérie Vivat, Krishnasamy Gunasekaran, Hinrich Gronemeyer, William Bourguet, Pierre Germain
Software Mentions: 2
Published: over 9 years ago

10.1007/s00253-017-8161-4

Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains
Cited by: 8
Author(s): Jonas Ramoni, Martina Marchetti‐Deschmann, Verena Seidl‐Seiboth, Bernhard Schink
Software Mentions: 2
Published: over 7 years ago

10.1007/s13205-014-0216-y

Computational pipeline to identify and characterize functional mutations in ornithine transcarbamylase deficiency
Cited by: 6
Author(s): R. Magesh, C. George Priya Doss
Software Mentions: 2
Published: over 10 years ago

10.1107/S139900471501857X

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography
Cited by: 50
Author(s): Takanori Nakane, Changyong Song, Mamoru Suzuki, Eriko Nango, Jun Kobayashi, Tetsuya Masuda, Shiro Inoue, Eiichi Mizohata, Toru Nakatsu, Tomoyuki Tanaka, Rie Tanaka, Tatsuro Shimamura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, So Iwata, Michihiro Sugahara
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0056742

Towards Improved Quality of GPCR Models by Usage of Multiple Templates and Profile-Profile Comparison
Cited by: 50
Author(s): Dorota Latek, Paweł Pasznik, Teresa Carlomagno, Sławomir Filipek
Software Mentions: 2
Published: over 11 years ago

10.1107/S2059798319006831

Structural and functional characterization of CMP-<i>N</i>-acetylneuraminate synthetase from<i>Vibrio cholerae</i>
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0086050

Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold
Cited by: 18
Author(s): John D. Steemson, Matthias Baake, Jasna Rakonjac, Vickery L. Arcus, Mark T. Liddament
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0039850

Structural Modeling and DNA Binding Autoinhibition Analysis of Ergp55, a Critical Transcription Factor in Prostate Cancer
Cited by: 3
Author(s): S.P. Gangwar, Sharmistha Dey, Ajay K. Saxena
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798318017825

Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with <i>Phaser</i>: human Rab27a
Cited by: 8
Author(s): Mostafa Jamshidiha, Inmaculada Pérez‐Dorado, James W. Murray, Edward W. Tate, Ernesto Cota, Randy J. Read
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0076355

Crystal Structure of the Human Short Coiled Coil Protein and Insights into SCOC-FEZ1 Complex Formation
Cited by: 6
Author(s): Caroline Behrens, Beyenech Binotti, Carla Schmidt, Carol V. Robinson, John Jia En Chua, Karin Kühnel
Software Mentions: 2
Published: about 11 years ago

10.1128/AEM.00390-19

Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase <i>In Vitro</i>
Cited by: 18
Author(s): Peter L. Herzog, Leander Sützl, Beate Eisenhut, Daniel Maresch, Dietmar Haltrich, Christian Obinger, Clemens K. Peterbauer
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0044124

Complex Structure of Engineered Modular Domains Defining Molecular Interaction between ICAM-1 and Integrin LFA-1
Cited by: 3
Author(s): Sungkwon Kang, Chae Un Kim, Xiaoling Gu, Róisı́n M. Owens, Sarah J. van Rijn, Vanissra Boonyaleepun, Yuxin Mao, Timothy A. Springer, Moonsoo M. Jin
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0081526

Structural Insights into the Mechanism for Recognizing Substrate of the Cytochrome P450 Enzyme TxtE
Cited by: 18
Author(s): Feng Yu, Minjun Li, Chunyan Xu, Zhijun Wang, Huan Zhou, Min Yang, Yaxing Chen, Lin Tang, Jianhua He
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0026792

Novel Adiponectin Variants Identified in Type 2 Diabetic Patients Reveal Multimerization and Secretion Defects
Cited by: 13
Author(s): Prapaporn Jungtrakoon, Nattachet Plengvidhya, Watip Tangjittipokin, Sarin Chimnaronk, Wanisa Salaemae, Nalinee Chongjaroen, Kanjana Chanprasert, Jatuporn Sujjitjoon, Chatchawan Srisawat, Pa‐thai Yenchitsomanus
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0008949

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Cited by: 26
Author(s): Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin Miller
Software Mentions: 2
Published: almost 15 years ago

10.1038/s42003-018-0123-6

In situ serial crystallography for rapid de novo membrane protein structure determination
Cited by: 26
Author(s): Chia-Ying Huang, V. Oliéric, Nicole Howe, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Lutz Vogeley, Shibom Basu, Kay Diederichs, Martin Caffrey, Meitian Wang
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0045379

BioFET-SIM Web Interface: Implementation and Two Applications
Cited by: 10
Author(s): Martin R. Hediger, Jan H. Jensen, Luca De Vico
Software Mentions: 2
Published: about 12 years ago

10.1128/AEM.01692-19

Crystal Structure of the Catalytic and Cytochrome <i>b</i> Domains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase
Cited by: 15
Author(s): Kouta Takeda, Takuya Ishida, Makoto Yoshida, Masahiro Samejima, Hiroyuki Ohno, Kiyohiko Igarashi, Nobuhumi Nakamura
Software Mentions: 2
Published: almost 5 years ago

10.1107/S2059798319010027

Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX
Cited by: 11
Author(s): Katarina Koruza, Bénédicte Lafumat, Maria Nyblom, Brian P. Mahon, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: over 5 years ago

10.1107/S2059798315023116

Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects
Cited by: 11
Author(s): Christian Reichen, Chaithanya Madhurantakam, Simon Hansen, Markus G. Grütter, Andreas Plückthun, Peer R. E. Mittl
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0193760

MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees
Cited by: 10
Author(s): Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin, Jean-Stéphane Venisse
Software Mentions: 2
Published: over 6 years ago

10.1107/S0907444910007493

Features and development of <i>Coot</i>
Cited by: 21,554
Author(s): Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan
Software Mentions: 2
Published: over 14 years ago

10.1107/S2059798317018289

The deduced role of a chitinase containing two nonsynergistic catalytic domains
Cited by: 16
Author(s): Tian Liu, Weixing Zhu, Jing Wang, Yong Zhou, Yanwei Duan, Mingli Qu, Qing Yang
Software Mentions: 2
Published: almost 7 years ago

10.1107/S0907444913011438

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement
Cited by: 7
Author(s): Debora L. Makino, Elena Conti
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0039993

Analysis of Conformational Variation in Macromolecular Structural Models
Cited by: 6
Author(s): Sandeep Srivastava, S Gayathri, Babu A. Manjasetty, B. Gopal
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0075992

Ligand Pose and Orientational Sampling in Molecular Docking
Cited by: 123
Author(s): Ryan G. Coleman, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0216427

Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain
Cited by: 22
Author(s): Md. Imran Khan, Deepu Dowarha, Revansiddha Katte, Ruey Hwang Chou, Anna Filipek, Chin Yu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0242686

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ
Cited by: 12
Author(s): William C. Scott, Brian Lowrance, Alexander C Anderson, Joel T. Weadge
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0152049

On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion
Cited by: 8
Author(s): Àlex L. González, Jordi Teixidó, José I. Borrell, Roger Estrada‐Tejedor
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0099408

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes
Cited by: 16
Author(s): Laura J. Kingsley, Markus A. Lill
Software Mentions: 2
Published: over 10 years ago

10.1007/s13205-014-0274-1

Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae
Cited by: 13
Author(s): Mohd Shahbaaz, Faizan Ahmad
Software Mentions: 2
Published: almost 10 years ago

10.1107/S2059798317015236

The crystal structure of the<i>Yersinia pestis</i>iron chaperone YiuA reveals a basic triad binding motif for the chelated metal
Cited by: 5
Author(s): C.D. Radka, Dongquan Chen, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0225244

Establishment of the experimental procedure for prediction of conjugation capacity in mutant UGT1A1
Cited by: 5
Author(s): Yutaka Takaoka, Atsuko Takeuchi, Aki Sugano, Kenji Miura, Mika Ohta, Takashi Suzuki, Daisuke Kobayashi, Takuji Kimura, Juichi Sato, Nobutaro Ban, Hisahide Nishio, Toshiyuki Sakaeda
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0210842

Potent, multi-target serine protease inhibition achieved by a simplified β-sheet motif
Cited by: 7
Author(s): Xingchen Chen, Blake T. Riley, Simon J. de Veer, David E. Hoke, Jessica Van Haeften, Darren Leahy, Joakim E. Swedberg, Maria Brattsand, Perry J. Hartfield, Ashley M. Buckle, Jonathan M. Harris
Software Mentions: 2
Published: almost 6 years ago

10.1089/ars.2017.7104

Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens
Cited by: 33
Author(s): Makrina Totsika, Dimitrios Vagenas, Jason J. Paxman, Geqing Wang, Rabeb Dhouib, Pooja Sharma, Jennifer L. Martin, M.J. Scanlon, Begoña Heras
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0255736

Network pharmacology and molecular docking reveal the effective substances and active mechanisms of Dalbergia Odoriferain protecting against ischemic stroke
Cited by: 3
Author(s): Kedi Liu, Xingru Tao, Jing Su, Fĕi Li, Fei Mu, S. J. Zhao, Xinming Lu, Jing Li, Sha Chen, Taiwei Dong, Jialin Duan, Peifeng Wei, Miaomiao Xi
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0097519

Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication
Cited by: 11
Author(s): Priscila da Silva Figueiredo Celestino Gomes, Nicolas Panel, Élodie Laine, Pedro Geraldo Pascutti, Éric Solary, Luba Tchertanov
Software Mentions: 2
Published: over 10 years ago

10.1107/S2059798315021683

<i>In meso in situ</i>serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Cited by: 89
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Nicole Howe, Lutz Vogeley, Xiangyu Liu, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Brian K. Kobilka, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 2
Published: almost 9 years ago

10.1107/S2059798320016368

Macromolecular crystallography using microcrystal electron diffraction
Cited by: 9
Author(s): Max T. B. Clabbers, Hongyi Xu
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0076803

Elucidation of Substrate Specificity in Aspergillus nidulans UDP-Galactose-4-Epimerase
Cited by: 7
Author(s): Sean A. Dalrymple, Jennifer S. Ko, I. S. Sheoran, Susan G. W. Kaminskyj, D.A.R. Sanders
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0158702

Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale
Cited by: 13
Author(s): Bikash R. Sahoo, Toshimichi Fujiwara
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0021507

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins
Cited by: 55
Author(s): Daniel J. Rigden, Duncan David Woodhead, Prudence W. H. Wong, Michael Y. Galperin
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0089027

Distinct Structural Features of the Peroxide Response Regulator from Group A Streptococcus Drive DNA Binding
Cited by: 13
Author(s): Chang Hong Lin, Shi-Yu Chao, Michal Hammel, Jay C. Nix, Hsiao-Ling Tseng, Chih-Cheng Tsou, Chun-Hsien Fei, Huo-Sheng Chiou, U‐Ser Jeng, Yee‐Shin Lin, Woei‐Jer Chuang, Jiunn-Jong Wu, Shuying Wang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0050097

Structure of the Human Discs Large 1 PDZ2– Adenomatous Polyposis Coli Cytoskeletal Polarity Complex: Insight into Peptide Engagement and PDZ Clustering
Cited by: 8
Author(s): Kevin C. Slep
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0139137

Engineering Streptavidin and a Streptavidin-Binding Peptide with Infinite Binding Affinity and Reversible Binding Capability: Purification of a Tagged Recombinant Protein to High Purity via Affinity-Driven Thiol Coupling
Cited by: 10
Author(s): Dawson Fogen, Sau‐Ching Wu, Kenneth Ng, Sui‐Lam Wong
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0061327

Prospecting for Novel Plant-Derived Molecules of Rauvolfia serpentina as Inhibitors of Aldose Reductase, a Potent Drug Target for Diabetes and Its Complications
Cited by: 46
Author(s): Shivalika Pathania, Vinay Randhawa, Ganesh Bagler
Software Mentions: 2
Published: over 11 years ago

10.1107/S2059798319009574

Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction
Cited by: 4
Author(s): Hsien‐Wei Yeh, Kuan Hung Lin, S.Y. Lyu, Yi Shan Li, Chun Man Huang, Yung Lin Wang, Hao Wei Shih, N.S. Hsu, Chang Jer Wu, Tsung Lin Li
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0241912

Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway
Cited by: 2
Author(s): Masanori Kohno, T. Arakawa, Naoki Sunagawa, Tetsuya Mori, Kiyohiko Igarashi, Tetsuya Nishimoto, Shinya Fushinobu
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0073962

The Human Minor Histocompatibility Antigen1 Is a RhoGAP
Cited by: 28
Author(s): Bart Jan de Kreuk, Antje Schaefer, Eloise C. Anthony, Simon Tol, Mar Fernandez‐Borja, Dirk Geerts, J. Pool, Lothar Hambach, Els Goulmy, Peter L. Hordijk
Software Mentions: 2
Published: about 11 years ago